Incidental Mutation 'R2392:Col9a2'
| ID |
247796 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Col9a2
|
| Ensembl Gene |
ENSMUSG00000028626 |
| Gene Name |
collagen, type IX, alpha 2 |
| Synonyms |
Col9a-2 |
| MMRRC Submission |
040360-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R2392 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
4 |
| Chromosomal Location |
120896763-120912522 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to G
at 120911455 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Glycine
at position 599
(R599G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000030372
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030372]
[ENSMUST00000058754]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000030372
AA Change: R599G
PolyPhen 2
Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000030372
Gene: ENSMUSG00000028626
AA Change: R599G
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
22 |
N/A |
INTRINSIC |
|
Pfam:Collagen
|
24 |
82 |
7.3e-12 |
PFAM |
|
Pfam:Collagen
|
59 |
115 |
2.4e-10 |
PFAM |
|
Pfam:Collagen
|
113 |
170 |
2e-8 |
PFAM |
|
Pfam:Collagen
|
176 |
236 |
8.9e-11 |
PFAM |
|
low complexity region
|
258 |
277 |
N/A |
INTRINSIC |
|
low complexity region
|
288 |
315 |
N/A |
INTRINSIC |
|
Pfam:Collagen
|
357 |
435 |
4.4e-8 |
PFAM |
|
Pfam:Collagen
|
459 |
523 |
6.1e-11 |
PFAM |
|
Pfam:Collagen
|
548 |
610 |
4.5e-11 |
PFAM |
|
low complexity region
|
639 |
661 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000058754
|
| SMART Domains |
Protein: ENSMUSP00000053900
Gene: ENSMUSG00000043207
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Peptidase_M48_N
|
41 |
225 |
2.5e-70 |
PFAM |
|
Pfam:Peptidase_M48
|
228 |
473 |
5.5e-75 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000140119
|
| Meta Mutation Damage Score |
0.3183 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.5%
- 10x: 97.0%
- 20x: 94.1%
|
| Validation Efficiency |
96% (53/55) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes one of the three alpha chains of type IX collagen, the major collagen component of hyaline cartilage. Type IX collagen, a heterotrimeric molecule, is usually found in tissues containing type II collagen, a fibrillar collagen. This chain is unusual in that, unlike the other two type IX alpha chains, it contains a covalently attached glycosaminoglycan side chain. Mutations in this gene are associated with multiple epiphyseal dysplasia. [provided by RefSeq, Jul 2008]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 53 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca12 |
A |
T |
1: 71,297,264 (GRCm39) |
S2409T |
probably damaging |
Het |
| Acap2 |
A |
G |
16: 30,958,458 (GRCm39) |
F120S |
probably damaging |
Het |
| Akr1c6 |
A |
G |
13: 4,484,477 (GRCm39) |
|
probably null |
Het |
| Bptf |
C |
A |
11: 106,963,573 (GRCm39) |
A1874S |
probably damaging |
Het |
| Ccnl1 |
A |
G |
3: 65,856,173 (GRCm39) |
V244A |
probably damaging |
Het |
| Cenpe |
T |
G |
3: 134,953,874 (GRCm39) |
L1628R |
probably damaging |
Het |
| Cfap54 |
A |
G |
10: 92,860,873 (GRCm39) |
|
probably null |
Het |
| Chchd7 |
T |
A |
4: 3,943,381 (GRCm39) |
|
probably null |
Het |
| Crybg2 |
G |
T |
4: 133,799,925 (GRCm39) |
V362L |
probably benign |
Het |
| Ddx11 |
T |
A |
17: 66,456,968 (GRCm39) |
V791E |
probably damaging |
Het |
| Disp1 |
G |
A |
1: 182,868,731 (GRCm39) |
P1230S |
probably benign |
Het |
| Elp5 |
T |
C |
11: 69,865,928 (GRCm39) |
H116R |
probably benign |
Het |
| Epb42 |
T |
C |
2: 120,860,468 (GRCm39) |
E177G |
possibly damaging |
Het |
| F13a1 |
T |
A |
13: 37,127,971 (GRCm39) |
I336F |
possibly damaging |
Het |
| Fabp3 |
C |
T |
4: 130,206,180 (GRCm39) |
T57I |
probably benign |
Het |
| Fcsk |
A |
G |
8: 111,616,356 (GRCm39) |
M453T |
probably benign |
Het |
| Hacd2 |
A |
T |
16: 34,926,748 (GRCm39) |
E249V |
probably benign |
Het |
| Hnrnpf |
C |
A |
6: 117,901,829 (GRCm39) |
A371D |
possibly damaging |
Het |
| Jmjd1c |
A |
G |
10: 67,065,683 (GRCm39) |
T1703A |
probably damaging |
Het |
| Kcnj13 |
G |
A |
1: 87,314,622 (GRCm39) |
T200I |
possibly damaging |
Het |
| Kif1b |
G |
A |
4: 149,305,077 (GRCm39) |
T949M |
possibly damaging |
Het |
| Klhl35 |
G |
A |
7: 99,123,031 (GRCm39) |
A552T |
possibly damaging |
Het |
| Krt74 |
A |
G |
15: 101,665,236 (GRCm39) |
|
noncoding transcript |
Het |
| Krtap14 |
T |
A |
16: 88,622,597 (GRCm39) |
|
probably null |
Het |
| Lrrc45 |
A |
G |
11: 120,610,365 (GRCm39) |
N492S |
probably benign |
Het |
| Lrrcc1 |
T |
A |
3: 14,601,580 (GRCm39) |
N114K |
probably damaging |
Het |
| Mfsd2b |
T |
C |
12: 4,915,164 (GRCm39) |
D375G |
possibly damaging |
Het |
| Mgat4a |
A |
G |
1: 37,537,785 (GRCm39) |
L44P |
probably damaging |
Het |
| Mttp |
A |
C |
3: 137,800,782 (GRCm39) |
D774E |
probably damaging |
Het |
| Myo5a |
T |
C |
9: 75,116,521 (GRCm39) |
V1554A |
probably benign |
Het |
| Nes |
C |
T |
3: 87,883,250 (GRCm39) |
A503V |
probably benign |
Het |
| Nme8 |
A |
G |
13: 19,873,113 (GRCm39) |
|
probably null |
Het |
| Nr4a1 |
A |
G |
15: 101,172,075 (GRCm39) |
D583G |
possibly damaging |
Het |
| Or12d17 |
A |
G |
17: 37,777,310 (GRCm39) |
Y71C |
probably damaging |
Het |
| Or5k14 |
A |
G |
16: 58,692,797 (GRCm39) |
S239P |
probably damaging |
Het |
| Pnpla8 |
T |
A |
12: 44,358,287 (GRCm39) |
L746I |
probably damaging |
Het |
| Ppp1r7 |
A |
T |
1: 93,282,063 (GRCm39) |
I205F |
probably benign |
Het |
| Psd4 |
C |
A |
2: 24,284,679 (GRCm39) |
P181Q |
probably damaging |
Het |
| Ripor2 |
G |
A |
13: 24,890,206 (GRCm39) |
V694I |
probably benign |
Het |
| Scn10a |
A |
G |
9: 119,456,268 (GRCm39) |
S1185P |
possibly damaging |
Het |
| Sec23b |
T |
A |
2: 144,427,507 (GRCm39) |
|
probably null |
Het |
| Slfn2 |
A |
G |
11: 82,956,154 (GRCm39) |
N12S |
possibly damaging |
Het |
| Slfn4 |
A |
G |
11: 83,076,248 (GRCm39) |
K38R |
possibly damaging |
Het |
| Smarca2 |
G |
T |
19: 26,618,050 (GRCm39) |
|
probably null |
Het |
| Taar4 |
A |
G |
10: 23,837,172 (GRCm39) |
T261A |
possibly damaging |
Het |
| Tbl2 |
A |
G |
5: 135,185,368 (GRCm39) |
D159G |
probably benign |
Het |
| Tmem120a |
T |
C |
5: 135,770,892 (GRCm39) |
E55G |
probably damaging |
Het |
| Ttc21b |
A |
G |
2: 66,037,794 (GRCm39) |
|
probably null |
Het |
| Vill |
A |
T |
9: 118,896,628 (GRCm39) |
|
probably benign |
Het |
| Vmn2r28 |
A |
T |
7: 5,487,130 (GRCm39) |
M511K |
probably damaging |
Het |
| Vmn2r81 |
A |
T |
10: 79,110,516 (GRCm39) |
D543V |
probably damaging |
Het |
| Wdr95 |
A |
G |
5: 149,504,135 (GRCm39) |
T314A |
probably benign |
Het |
| Zbtb8b |
A |
G |
4: 129,326,982 (GRCm39) |
I61T |
probably damaging |
Het |
|
| Other mutations in Col9a2 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01331:Col9a2
|
APN |
4 |
120,902,389 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
IGL01978:Col9a2
|
APN |
4 |
120,901,863 (GRCm39) |
missense |
unknown |
|
|
IGL01995:Col9a2
|
APN |
4 |
120,907,607 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL02162:Col9a2
|
APN |
4 |
120,911,531 (GRCm39) |
unclassified |
probably benign |
|
|
IGL02931:Col9a2
|
APN |
4 |
120,910,389 (GRCm39) |
missense |
probably benign |
0.06 |
|
collision
|
UTSW |
4 |
120,906,913 (GRCm39) |
critical splice donor site |
probably null |
|
|
gravity_wave
|
UTSW |
4 |
120,901,216 (GRCm39) |
critical splice donor site |
probably null |
|
|
R0208:Col9a2
|
UTSW |
4 |
120,909,485 (GRCm39) |
splice site |
probably benign |
|
|
R0426:Col9a2
|
UTSW |
4 |
120,901,857 (GRCm39) |
splice site |
probably benign |
|
|
R0512:Col9a2
|
UTSW |
4 |
120,911,504 (GRCm39) |
missense |
probably benign |
0.22 |
|
R0973:Col9a2
|
UTSW |
4 |
120,896,985 (GRCm39) |
critical splice donor site |
probably null |
|
|
R1023:Col9a2
|
UTSW |
4 |
120,901,207 (GRCm39) |
missense |
unknown |
|
|
R1657:Col9a2
|
UTSW |
4 |
120,898,171 (GRCm39) |
missense |
unknown |
|
|
R1724:Col9a2
|
UTSW |
4 |
120,911,099 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2171:Col9a2
|
UTSW |
4 |
120,902,198 (GRCm39) |
nonsense |
probably null |
|
|
R2206:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2221:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2223:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2273:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2274:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2275:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2354:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2393:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2394:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R3421:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R3426:Col9a2
|
UTSW |
4 |
120,907,604 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R3710:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R3821:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R3838:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R3839:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R4067:Col9a2
|
UTSW |
4 |
120,909,586 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4298:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R4299:Col9a2
|
UTSW |
4 |
120,911,455 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R4595:Col9a2
|
UTSW |
4 |
120,902,352 (GRCm39) |
missense |
probably benign |
0.04 |
|
R4942:Col9a2
|
UTSW |
4 |
120,910,316 (GRCm39) |
missense |
possibly damaging |
0.73 |
|
R5120:Col9a2
|
UTSW |
4 |
120,896,969 (GRCm39) |
missense |
unknown |
|
|
R5434:Col9a2
|
UTSW |
4 |
120,898,162 (GRCm39) |
nonsense |
probably null |
|
|
R6143:Col9a2
|
UTSW |
4 |
120,911,060 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7027:Col9a2
|
UTSW |
4 |
120,901,216 (GRCm39) |
critical splice donor site |
probably null |
|
|
R7056:Col9a2
|
UTSW |
4 |
120,906,913 (GRCm39) |
critical splice donor site |
probably null |
|
|
R7417:Col9a2
|
UTSW |
4 |
120,911,489 (GRCm39) |
missense |
not run |
|
|
R7571:Col9a2
|
UTSW |
4 |
120,896,981 (GRCm39) |
missense |
unknown |
|
|
R9120:Col9a2
|
UTSW |
4 |
120,900,951 (GRCm39) |
splice site |
probably benign |
|
|
R9341:Col9a2
|
UTSW |
4 |
120,911,483 (GRCm39) |
missense |
probably benign |
0.03 |
|
R9343:Col9a2
|
UTSW |
4 |
120,911,483 (GRCm39) |
missense |
probably benign |
0.03 |
|
R9389:Col9a2
|
UTSW |
4 |
120,911,948 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9527:Col9a2
|
UTSW |
4 |
120,899,528 (GRCm39) |
critical splice donor site |
probably null |
|
|
R9620:Col9a2
|
UTSW |
4 |
120,910,403 (GRCm39) |
critical splice donor site |
probably null |
|
|
R9784:Col9a2
|
UTSW |
4 |
120,898,226 (GRCm39) |
missense |
unknown |
|
|
Z1176:Col9a2
|
UTSW |
4 |
120,910,994 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- TACAGAACCTCCCAAATCTTATCTGG -3'
(R):5'- TCAAGAGTCCCAACTGCCAG -3'
Sequencing Primer
(F):5'- AACCTCCCAAATCTTATCTGGATCTC -3'
(R):5'- AGAGACACCTCCAGCTTGG -3'
|
| Posted On |
2014-11-11 |
Incidental Mutation